def print_foot(out, options, start_time):
'''Output the foot information in the output file'''
linesep = os.linesep
out.append('#' * 80 + linesep)
elapsed_time = time.time() - start_time
out.append('InFile: '.rjust(42) + os.path.basename(options.infile.name))
out.append('OutFile: '.rjust(42) + os.path.basename(options.outfile.name))
if options.amplicon:
out.append('OutAmpliconFile: '.rjust(42) + '%s.fa' % (options.outfile.name))
out.append('Database: '.rjust(42) + textwrap.fill(', '.join([os.path.basename(db) for db in options.database]), 80))
out.append('Degenerate: '.rjust(42) + degenerate.capitalize())
out.append('k value: '.rjust(42) + str(options.k_value) + linesep)
out.append('Concentration of monovalent cations [mM]: '.rjust(42) + str(options.mono_conc))
out.append('Concentration of divalent cations [mM]: '.rjust(42) + str(options.diva_conc))
out.append('Concentration of annealing oligos [nM]: '.rjust(42) + str(options.oligo_conc))
out.append('Concentration of dNTPs [mM]: '.rjust(42) + str(options.dntp_conc) + linesep)
out.append('PPC cutoff [%]: '.rjust(42) + str(options.ppc))
out.append('Size start [bp]: '.rjust(42) + str(options.size_start))
out.append('Size stop [bp]: '.rjust(42) + str(options.size_stop))
out.append(('Tm start [%s]: ' % (u'\u2103')).rjust(41) + str(options.tm_start))
if options.tm_stop == sys.maxint:
tm_stop = 'Unlimited'
else:
tm_stop = options.tm_stop
if options.dg_start == -sys.maxint:
dg_start = 'Unlimited'
else:
dg_start = options.dg_start
out.append(('Tm stop [%s]: ' % (u'\u2103')).rjust(41) + str(tm_stop))
# It seems that ΔG only occupied 1.5 space
out.append(('%sG start [kcal/mol]: ' % (u'\u0394')).rjust(41) + str(dg_start))
out.append(('%sG stop [kcal/mol]: ' % (u'\u0394')).rjust(41) + str(options.dg_stop))
#out.append(linesep)
#out.append('Command and options: ')
#full_cmd = ' '.join(sys.argv)
#out.append(' ' + textwrap.fill(full_cmd, 80))
out.append(linesep)
if elapsed_time < 1:
out.append('Time used: ' + '%.2f s' % elapsed_time)
else:
out.append('Time used: ' + '%s m %s s' % chilli.seconds2min_sec(int(elapsed_time)))
out.append('Date: %s' % chilli.format_show_time())
out.append(linesep)
return out
def print_foot(out, options, start_time):
'''Output the foot information in the output file'''
linesep = os.linesep
out.append('#' * 80 + linesep)
elapsed_time = time.time() - start_time
out.append('InFile: '.rjust(42) + os.path.basename(options.infile.name))
out.append('OutFile: '.rjust(42) + os.path.basename(options.outfile.name))
if options.amplicon:
out.append('OutAmpliconFile: '.rjust(42) + '%s.fa' %
(options.outfile.name))
out.append('Database: '.rjust(42) + textwrap.fill(
', '.join([os.path.basename(db) for db in options.database]), 80))
out.append('Degenerate: '.rjust(42) + degenerate.capitalize())
out.append('k value: '.rjust(42) + str(options.k_value) + linesep)
out.append('Concentration of monovalent cations [mM]: '.rjust(42) +
str(options.mono_conc))
out.append('Concentration of divalent cations [mM]: '.rjust(42) +
str(options.diva_conc))
out.append('Concentration of annealing oligos [nM]: '.rjust(42) +
str(options.oligo_conc))
out.append('Concentration of dNTPs [mM]: '.rjust(42) +
str(options.dntp_conc) + linesep)
out.append('PPC cutoff [%]: '.rjust(42) + str(options.ppc))
out.append('Size start [bp]: '.rjust(42) + str(options.size_start))
out.append('Size stop [bp]: '.rjust(42) + str(options.size_stop))
out.append(('Tm start [%s]: ' % (u'\u2103')).rjust(41) +
str(options.tm_start))
if options.tm_stop == sys.maxint:
tm_stop = 'Unlimited'
else:
tm_stop = options.tm_stop
if options.dg_start == -sys.maxint:
dg_start = 'Unlimited'
else:
dg_start = options.dg_start
out.append(('Tm stop [%s]: ' % (u'\u2103')).rjust(41) + str(tm_stop))
# It seems that ΔG only occupied 1.5 space
out.append(('%sG start [kcal/mol]: ' % (u'\u0394')).rjust(41) +
str(dg_start))
out.append(('%sG stop [kcal/mol]: ' % (u'\u0394')).rjust(41) +
str(options.dg_stop))
#out.append(linesep)
#out.append('Command and options: ')
#full_cmd = ' '.join(sys.argv)
#out.append(' ' + textwrap.fill(full_cmd, 80))
out.append(linesep)
if elapsed_time < 1:
out.append('Time used: ' + '%.2f s' % elapsed_time)
else:
out.append('Time used: ' +
'%s m %s s' % chilli.seconds2min_sec(int(elapsed_time)))
out.append('Date: %s' % chilli.format_show_time())
out.append(linesep)
return out
def single_mode():
"""Single mode"""
error = None
session_dir = chilli.session(session_parent)
if request.method == 'POST':
database = request.form['db_selected']
db_list = [os.path.join(MFEprimerDB, db) for db in database.split(':')]
infile = os.path.join(session_dir, 'query.fa')
fh = open(infile, 'w')
seq_sn = 1
seq_list = []
while request.form.has_key("seq%d" % seq_sn):
seq = request.form["seq%d" % seq_sn]
seq = re.sub('^[^a-zA-Z]+|[^a-zA-Z]+$', '', seq) # Remove additional chars, such as 5'- 3'-
seq = re.sub('\s', '', seq) # Remove spaces in sequence. Thanks anonymous reviewers.
if seq:
seq_list.append(seq)
fh.write(">Seq%s\n%s\n" % (seq_sn, seq))
seq_sn += 1
fh.close()
if len(seq_list) < 2:
error = 'Need two or more primer sequences'
return render_template('index.html', error=error)
error_or_degenerate = SeqCheck.fasta_format_check(open(infile), err_path='here')
if error_or_degenerate in ['yes', 'no']:
degenerate = error_or_degenerate
else:
return render_template('index.html', error=error_or_degenerate)
Tm_upper_limit = float(request.form['Tm_upper_limit'])
Tm_lower_limit = float(request.form['Tm_lower_limit'])
size_upper_limit = int(request.form['size_upper_limit'])
size_lower_limit = int(request.form['size_lower_limit'])
if size_lower_limit < 0 or size_upper_limit > 100000:
error = 'Size range should be in [0, 100000]'
return render_template('index.html', error=error)
ppc_lower_limit = float(request.form['ppc_lower_limit'])
if ppc_lower_limit < 0 or ppc_lower_limit > 100:
error = 'PPC lower cutoff should be in (0, 100)'
return render_template('index.html', error=error)
mv = float(request.form['mono_conc'])
dv = float(request.form['diva_conc'])
dntp = float(request.form['dntp_conc'])
oligo = float(request.form['oligo_conc'])
session['db_selected'] = ':'.join([os.path.basename(str(db)) for db in db_list])
options = OptionCreator(db_list,
infile,
Tm_upper_limit,
Tm_lower_limit,
size_upper_limit,
size_lower_limit,
ppc_lower_limit,
mv,
dv,
dntp,
oligo,
degenerate,
)
start_time = time.time()
amp_list, oligos = MFEprimer.process_primer(options, session_dir)
detail, size_dict, tm_dict, dg_dict = format_output_primer(amp_list, oligos, options, start_time, session_dir)
if len(detail) > hist_cutoff:
size_hist_keys = size_hist.keys()
size_hist_keys.sort(reverse=True)
for size, num in size_dict.items():
for hist_key in size_hist_keys:
if int(size) > hist_key:
break
size_hist[hist_key] += num
tm_hist_keys = tm_hist.keys()
tm_hist_keys.sort(reverse=True)
for tm, num in tm_dict.items():
for hist_key in tm_hist_keys:
if float(tm) > hist_key:
break
tm_hist[hist_key] += num
dg_hist_keys = dg_hist.keys()
dg_hist_keys.sort(reverse=False)
for dg, num in dg_dict.items():
for hist_key in dg_hist_keys:
if float(dg) < float(hist_key):
break
dg_hist[hist_key] += num
new_dg_hist = {}
for key, value in dg_hist.items():
new_dg_hist[str(key)] = value
database = ', '.join([os.path.basename(db).capitalize() for db in options.database])
oligos = format_oligos(oligos, options)
elapsed_time = time.time() - start_time
if elapsed_time < 1:
print_elapsed_time = '%.2f s' % elapsed_time
else:
print_elapsed_time = '%s m %s s' % chilli.seconds2min_sec(int(elapsed_time))
return render_template('primer_output.html', options=options, database=database,
oligos=oligos, amp_num=len(amp_list), time_used=print_elapsed_time,
date=chilli.format_show_time(), citation=Citation, detail=detail,
session_dir=session_dir, size_hist=size_hist, tm_hist=tm_hist, dg_hist=new_dg_hist,
max_size_num = max([num for num in size_hist.values()]),
max_tm_num = max([num for num in tm_hist.values()]),
max_dg_num = max([num for num in dg_hist.values()]),
)
return redirect(url_for('root'))